Novel organic heterostructures fabricated with a bilayer consisting of an axially substituted silicon phthalocyanine (R 2 -SiPc) derivative and lutetium bis-phthalocyanine (LuPc 2 ) are investigated for their ammonia sensing properties. Surface and microstructure characterization of the heterostructure films reveal either compact or highly porous surface topography in (345F) 2 -SiPc and Cl 2 -SiPc-based heterostructures, while electrical characterization reveals a strong influence of the axial substituent in R 2 -SiPc on NH 3 sensing capabilities. Electrical characterization further demonstrates an apparent energy barrier for interfacial charge transport, which is higher in the (345F) 2 -SiPc/LuPc 2 heterojunction device. In-depth charge transport studies by impedance spectroscopy further reveal a resistive interface in (345F) 2 -SiPc/LuPc 2 and faster bulk and interfacial charge transport in Cl 2 -SiPc/LuPc 2 heterojunction devices. Different interfacial charge transport capabilities and surface topographies affect NH 3 sensing properties of the two heterojunction devices, in which (345F) 2 -SiPc/LuPc 2 reveals a fast and non-linear response with a limit of detection (LOD) of 310 ppb, while Cl 2 -SiPc/LuPc 2 exhibits a slow, and linear response to NH 3 with LOD of 100 ppb. Finally, different metrological parameters of the two sensors are correlated to the respective gas-material interactions, in which adsorption and diffusion regimes are modulated by the surface topography and hydrophobicity of the sensing layer.